ViewGene

Locus Name:
GeneID:
Location:

GeneID:1368
TrivialName: PA14_60890
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_60890
PAO1 Ortholog Locus:PA4602
Sequence Length:1254
Protein Length:417
Start: 5433207
Stop: 5434460
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07990.1|AE004874_3 (AE004874) serine hydroxymethyltransferase [Pseudomonas aeruginosa PAO1]
Identities = 414/417 (99%), Positives = 416/417 (99%)
Sequence:
ATGTTCAGCCGTGATTTGACCCTCGCCCGCTACGATGCCGAACTCTTTGCCGCGATGGAGCAGGAAGCCCAG
CGCCAGGAAGAGCACATCGAGCTGATCGCCTCCGAGAACTACACCAGCCCGGCGGTGATGGAAGCCCAGGGT
TCGGTGCTGACCAACAAGTACGCCGAAGGTTATCCGCACAAGCGCTACTACGGCGGCTGCGAGTACGTCGAT
ATCGTCGAGCAACTGGCCATCGACCGCGCCAAGCAACTGTTCGGCGCCGATTACGCCAACGTCCAGCCGCAC
GCCGGCTCCCAGGCCAACGCCGCGGTCTACCTGGCCCTGCTGTCGGCCGGCGACACCATCCTCGGCATGAGC
CTGGCCCACGGCGGCCACCTGACCCACGGCGCCAGCGTCTCCTCCTCCGGCAAGCTGTACAACGCCGTGCAG
TACGGCATCGACGCCAATGGCCTGATCGACTACGACGAAGTCGAGCGCCTGGCCGTGGAGCACAAGCCGAAG
ATGATCGTCGCCGGCTTCTCCGCCTATTCCCAGGTCCTCGATTTCGCCCGCTTCCGCGCCATCGCCGACAAG
GTCGGCGCCTACCTGTTCGTCGACATGGCCCACGTCGCCGGCCTGGTCGCCGCTGGCGTCTACCCGAACCCG
GTGCCGTTCGCCGACGTGGTCACCACCACCACCCACAAGACCCTGCGCGGTCCGCGCGGTGGCCTGATCCTG
GCGCGCGCCAACGAGGAGATCGAGAAGAAGCTCAACTCCGCGGTATTCCCCGGCGCCCAGGGCGGTCCGCTG
GAGCACGTGATCGCGGCCAAGGCGGTGTGCTTCAAGGAAGCCCTGCAGCCGGAGTTCAAGACCTACCAGCAG
CAGGTCCTGAAGAACGCCCAGACCATGGCCCAGGTCTTCCTCGACCGCGGTTTCGACGTGGTTTCCGGCGGC
ACCCAGAACCACCTGTTCCTGCTCTCCCTGATCAAGCAGGACATCACCGGCAAAGACGCCGACGCCGCCCTC
GGCCGCGCGTTCATCACCGTGAACAAGAACTCGGTCCCGAACGACCCGCGCTCGCCGTTCGTCACCTCCGGC
CTGCGCATCGGTACCCCGGCCGTGACCACCCGCGGCTTCAAGGAAGCCGAGTGCCGCGAGCTGGCCGGCTGG
ATCTGCGACATCCTCGAGAACATGGGCGACGAGTCCGTGGTCAACGGCGTACGCGAGAAGGTCAAGGCGATC
TGCGCCAAGTTCCCGGTCTACGGCAACTAA
Translation:
MFSRDLTLARYDAELFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYPHKRYYGGCEYVD
IVEQLAIDRAKQLFGADYANVQPHAGSQANAAVYLALLSAGDTILGMSLAHGGHLTHGASVSSSGKLYNAVQ
YGIDANGLIDYDEVERLAVEHKPKMIVAGFSAYSQVLDFARFRAIADKVGAYLFVDMAHVAGLVAAGVYPNP
VPFADVVTTTTHKTLRGPRGGLILARANEEIEKKLNSAVFPGAQGGPLEHVIAAKAVCFKEALQPEFKTYQQ
QVLKNAQTMAQVFLDRGFDVVSGGTQNHLFLLSLIKQDITGKDADAALGRAFITVNKNSVPNDPRSPFVTSG
LRIGTPAVTTRGFKEAECRELAGWICDILENMGDESVVNGVREKVKAICAKFPVYGN*
AnnotationID:1377GeneID:1368
AnnotatorUID: diggins
Modification Date/Time: 2005-05-06 07:07:29
Gene Name:glyA
Confidence Code:2
GeneProduct:Glycine/serine hydroxymethyltransferase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(2) Amino acid biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0112,pfam00464,KOG2467
Secondary Functional Category(ies):
EC Number:2.1.2.1
Status:ACTIVE
Pathway:
Homology:
>gb|AAN66296.1|AE016258_2 (AE016776) serine hydroxymethyltransferase [Pseudomonas putida
           KT2440]
          Length = 417

 Score =  773 bits (1996), Expect = 0.0
 Identities = 382/417 (91%), Positives = 403/417 (96%)


>gb|AAN81523.1|AE016764_205 (AE016764) Serine hydroxymethyltransferase [Escherichia coli
           CFT073]
          Length = 419

 Score =  639 bits (1649), Expect = 0.0
 Identities = 311/416 (74%), Positives = 361/416 (86%), Gaps = 1/416 (0%)
Structural Features:
COG0112, GlyA, Glycine/serine hydroxymethyltransferase 
[Amino acid transport and metabolism]
CD-Length = 413 residues,  98.8% aligned
Score =  681 bits (1758), Expect = 0.0
Identities = 287/411 (69%), Positives = 341/411 (82%), Gaps = 4/411 (0%)

pfam00464, SHMT, Serine hydroxymethyltransferase.
CD-Length = 397 residues, 100.0% aligned
Score =  570 bits (1471), Expect = 2e-163
Identities = 237/398 (59%), Positives = 293/398 (73%), Gaps = 21/398 (5%)

KOG2467, Glycine/serine hydroxymethyltransferase 
[Amino acid transport and metabolism]
CD-Length = 477 residues,  95.4% aligned
Score =  455 bits (1172), Expect = 9e-129
Identities = 210/456 (46%), Positives = 284/456 (62%), Gaps = 47/456 (10%)
Genomic Context:
Comment:
ReferenceID:2739
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:19884
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
ReferenceID:31621
Author/Investigator(s):
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:Misc (text/plain)
Data:1368_cdd.html
URL:
ReferenceID:33351
Author/Investigator(s): Simic P, Willuhn J, Sahm H, Eggeling L.
Title: Identification of glyA (encoding serine hydroxymethyltransferase) and its use together with the exporter ThrE to increase L-threonine accumulation by Corynebacterium glutamicum.
PubMed: 12089010
MedLine:
Source:
Appl Environ Microbiol. 2002 Jul;68(7):3321-7.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12089010
ReferenceID:33352
Author/Investigator(s): Lorenz E, Stauffer GV.
Title: RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli.
PubMed: 8757744
MedLine:
Source:
Microbiology. 1996 Jul;142 ( Pt 7):1819-24.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8757744
ReferenceID:33353
Author/Investigator(s): Chan VL, Bingham HL.
Title: Complete sequence of the Campylobacter jejuni glyA gene encoding serine hydroxymethyltransferase.
PubMed: 2060796
MedLine:
Source:
Gene. 1991 May 15;101(1):51-8.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2060796
ReferenceID:33354
Author/Investigator(s): Steiert JG, Urbanowski ML, Stauffer LT, Plamann MD, Stauffer GV.
Title: Nucleotide sequence of the Salmonella typhimurium glyA gene.
PubMed: 2134182
MedLine:
Source:
DNA Seq. 1990;1(2):107-13.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2134182
ReferenceID:33355
Author/Investigator(s): Chan VL, Bingham H, Kibue A, Nayudu PR, Penner JL.
Title: Cloning and expression of the Campylobacter jejuni glyA gene in Escherichia coli.
PubMed: 3072255
MedLine:
Source:
Gene. 1988 Dec 15;73(1):185-91.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3072255
ReferenceID:33356
Author/Investigator(s): Urbanowski ML, Plamann MD, Stauffer LT, Stauffer GV.
Title: Cloning and characterization of the gene for Salmonella typhimurium serine hydroxymethyltransferase.
PubMed: 6325301
MedLine:
Source:
Gene. 1984 Jan;27(1):47-54.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6325301
ReferenceID:33357
Author/Investigator(s): Plamann MD, Stauffer LT, Urbanowski ML, Stauffer GV.
Title: Complete nucleotide sequence of the E. coli glyA gene.
PubMed: 6300791
MedLine:
Source:
Nucleic Acids Res. 1983 Apr 11;11(7):2065-75.
Reference Type:Journal
Data:
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6300791
Homologs By Global Alignment
Gene ID:1368

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
2490 PA4602_tr translation of PA4602 417 99.28 99.76 0 2123.0
78685 gb|AAG07990.1|AE004874_3 (AE004874) serine hydroxymethyltransferase [Pseudomonas aeruginosa PAO1] 417 99.28 99.76 0 2123.0
78686 gb|AAN66296.1|AE016258_2 (AE016776) serine hydroxymethyltransferase [Pseudomonas putida KT2440] 417 91.60 96.64 0 1996.0
78687 gb|AAO58078.1| (AE016872) serine hydroxymethyltransferase [Pseudomonas syringae pv. tomato str. DC3000] 417 90.40 96.16 0 1976.0
78688 gb|AAN65953.1|AE016223_7 (AE016775) serine hydroxymethyltransferase [Pseudomonas putida KT2440] 418 82.05 88.75 2 1765.0
GC ORFID: 44370How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA4602Glimmer Score:
Start: 4696887Stop: 4698140
Length: 1254
Start Codon: ATGTruncated Start:
Stop Codon: TAATruncated Stop:
Homolog: t_PA4602 translation of PA4602Homolog Bit Score 822.0
Other Homologs: psyr_15may02_Scaffold4_revised_gene5644 (ORF: BLASTX 769.0), t_PA5415 (ORF: BLASTX 670.0), t_PA2444 (ORF: BLASTX 669.0), t_PA4602 (ORF: GLIMMER)
GC ORF Sequence
ATGTTCAGCCGTGATTTGACCCTCGCCCGCTACGATGCCGAACTCTTTGCCGCGATGGAGCAGGAAGCCCAG
CGCCAGGAAGAGCACATCGAGCTGATCGCCTCCGAGAACTACACCAGCCCGGCGGTGATGGAAGCCCAGGGT
TCGGTGCTGACCAACAAGTACGCCGAAGGTTATCCGCACAAGCGCTACTACGGCGGCTGCGAGTACGTCGAT
ATCGTCGAGCAACTGGCCATCGACCGCGCCAAGCAACTGTTCGGCGCCGATTACGCCAACGTCCAGCCGCAC
GCCGGCTCCCAGGCCAACGCCGCGGTCTACCTGGCCCTGCTGTCGGCCGGCGACACCATCCTCGGCATGAGC
CTGGCCCACGGCGGCCACCTGACCCACGGCGCCAGCGTCTCCTCCTCCGGCAAGCTGTACAACGCCGTGCAG
TACGGCATCGACGCCAATGGCCTGATCGACTACGACGAAGTCGAGCGCCTGGCCGTGGAGCACAAGCCGAAG
ATGATCGTCGCCGGCTTCTCCGCCTATTCCCAGGTCCTCGATTTCGCCCGCTTCCGCGCCATCGCCGACAAG
GTCGGCGCCTACCTGTTCGTCGACATGGCCCACGTCGCCGGCCTGGTCGCCGCTGGCGTCTACCCGAACCCG
GTGCCGTTCGCCGACGTGGTCACCACCACCACCCACAAGACCCTGCGCGGTCCGCGCGGTGGCCTGATCCTG
GCGCGCGCCAACGAGGAGATCGAGAAGAAGCTCAACTCCGCGGTATTCCCCGGCGCCCAGGGCGGTCCGCTG
GAGCACGTGATCGCGGCCAAGGCGGTGTGCTTCAAGGAAGCCCTGCAGCCGGAGTTCAAGACCTACCAGCAG
CAGGTCCTGAAGAACGCCCAGACCATGGCCCAGGTCTTCCTCGACCGCGGTTTCGACGTGGTTTCCGGCGGC
ACCCAGAACCACCTGTTCCTGCTCTCCCTGATCAAGCAGGACATCACCGGCAAAGACGCCGACGCCGCCCTC
GGCCGCGCGTTCATCACCGTGAACAAGAACTCGGTCCCGAACGACCCGCGCTCGCCGTTCGTCACCTCCGGC
CTGCGCATCGGTACCCCGGCCGTGACCACCCGCGGCTTCAAGGAAGCCGAGTGCCGCGAGCTGGCCGGCTGG
ATCTGCGACATCCTCGAGAACATGGGCGACGAGTCCGTGGTCAACGGCGTACGCGAGAAGGTCAAGGCGATC
TGCGCCAAGTTCCCGGTCTACGGCAACTAA